April 09, 2014

Svante Paabo talk at NIH

A very interesting bit is from 18:30 and forward, in which he discusses the 45,000y BP modern human from Ust-Ishim. Here is a screenshot from this part of the talk (20:32):

According to Dr. Paabo, Ust-Ishim has longer Neandertal chunks than modern humans and this can be used to estimate that the admixture with Neandertals happened 331+/-99 generations before its time of 45,000y BP, or around 50-60,000y BP.

The coalescence of mtDNA haplogroups M and N has been estimated as ~50 and ~59ky BP respectively using modern human variation, so this seems quite compatible with that. This pretty much proves that there were modern humans in Eurasia before the Upper Paleolithic revolution and disproves Richard Klein's theory that modern humans together with UP technologies spread Out-of-Africa only after 50,000 years ago.

111 comments:

"This pretty much proves that there were modern humans in Eurasia before the Upper Paleolithic revolution and disproves Richard Klein's theory that modern humans together with UP technologies spread Out-of-Africa only after 50,000 years ago".

I had numerous heated arguments with Maju on that subject (before he banned me from commenting at his blog). He insisted that modern humans could not have been present in Central Eurasia before the arrival there of the Upper Paleolithic. I hope he takes the time to look at this post.

A couple of interesting comments in the lecture. He is totally comfortable with the idea of admixture with some as yet unknown East Asian archaic human. And a passing comment that his lab has sequenced a small region of H. heidelbergensis from 400,000 years ago.

Clearly with less distance from Ust-Ishim, the correlation between Ust-Ishim sites and Karitiana sites increases to the point when they completely merge at roughly 0.1 distance. As the distance from Ust-Ishim increases, Han and Dai stay close to Ust-Ishim, while Karitiana diverges.

Also, it noticeable that the higher the correlation between Amerindians and Ust-Ishim, the higher it is for French and Sardinians as well suggesting, in line with MA-1 and other ancient West eurasian DNA results, that Amerindians form a common baseline for both West Eurasian and East Asians populations.

It's another good day for out-of-America!

An earlier frame showing chromosome 12 shows that Australians and Papuans are probably right there with Amerindians in terms of their closeness to Ust-Ishim.Again, this is consistent with other studies, such as Prufer on Altai Neandertal.

The presentation by Paabo was very interesting. I liked much of what he said but it appears that many of his comments are not supported by the archaeology. The major problems with his talk is the idea that Africans fail to share genes with Neanderthal,and that AMH entered western Eurasia from the Levant.

First archaeology indicates that the first Europeans entered Iberia and carried the Aurignacian culture from east to west. If we use evidence of the Aurignacian culture for the expansion of AMH to western Eurasia, the sites for this culture in the Levant are later than those for Europe.

Secondly, recent research indicates that the San share genes with the Altaic and Vinja (see video at 22:20) Neanderthals. And we also find that the Luhya carry neanderthal genes involved in lipi catabolism. All of this suggest that Africans do carry Neanderthal genes.

You'll have to explain how you come to that conclusion. I see the lecture as totally exploding the belief. Check out at 38 min. where he says ancient humans never crossed water. So what ancient humans are you proposing to have lived in America?

"An earlier frame showing chromosome 12 shows that Australians and Papuans are probably right there with Amerindians in terms of their closeness to Ust-Ishim".

And that proves Australians and Papuans emerged from America ... how?

"presumably most primates need to be like that since they brachiate"

Check the lecture again. You will see the change did not happen until humans/Neanderthals/Denisovans had split from the apes. Most primates therefore don't have the mutation.

"First archaeology indicates that the first Europeans entered Iberia and carried the Aurignacian culture from east to west".

You have failed to notice Dienekes' comment:

"This pretty much proves that there were modern humans in Eurasia before the Upper Paleolithic revolution"

In other words the Aurignacian developed long after humans had left Africa.

A 50,000-60,000 years BP admixture date would imply that admixture took place about 40,000-70,000 years after the earliest archaeological evidence of modern humans outside of Africa.

Thus, this suggests that this is picking up an admixture wave that probably took place only after modern humans had expanded out of the Levant and Arabia.

Indeed, 50,000-60,000 years ago is also probably after the split between proto-West Eurasians and proto-East Eurasians, and tends to favor the notion that Neanderthal admixture occurred in similar parallel admixture events after the West Eurasian-East Eurasian split, rather than in a single admixture event prior to that split.

Dr. WintersAn answer to you statement of African Neandertal genes may be found athttp://www.newscientist.com/article/dn24988-humanitys-forgotten-return-to-africa-revealed-in-dna.htmlIt is of European origin.

Foxp2 is found in Sapiens, Neanderthals and Denisovans. A nice piece of evidence that all three probably had language. It also suggests that their common ancestor, Heidelbergensis in Africa, probably had language also.-------His comments on Erectus and Heidelbergensis were very interesting. I have been assuming that Denisovans were either Heidelbergensis or Erectus, most probably the former. Now I am wondering if Floresiensis might be Denisovan. Found in South East Asia in just the right area, and so far as I know we have no genetics for our shortest near relative.-----Not quite sure what you are on about German. So far as I can tell everything merges at 0.1 cM. I read the Weighted CC data quite differently. Basically that the Neanderthal admixture had been in the Sardinian/French populations for longer, suggesting that the admixture was older in these populations than for the eastern modern populations. I think the younger ages of the admixture in Han2, Dai2 and Karitiana is due to a second admixture event (<700 generations ago) bringing the average down. As Paabo suggested. Variable levels of this admixture population would lead to population differences. And Karitiana were isolated from diluting population flows from the west.

In any case this puts the Karitiana in Neanderthal territory ~37 kya or even more recently. That is, in Eurasia, not the Americas.-----As a side note. I will be absolutely flabbergasted if we do not eventually find Neanderthal man in North Africa. They were numerous in Gibralter, and North Africa seems to have some similar types of environments, albeit a bit warmer. They were clearly present in the Middle East. I see no reason why they would NOT be in North Africa, probably in droves.

That makes a huge assumption strands break down at a steady rate which has no merit to it.

If some part of a strand is selected on then it's going to preserve the whole strand until by freak chance the strand breaks. This process is going to be many many times faster with large modern populations than with ancient ones.

Which goes more in line with multiregionalism. If you have already pushed out of africa back so far, it may as well be abandoned. Especially since while the strand sizes are bigger, they don't cotain the same genes that are preserved today.

This idea of single admixture event is ridiculous one that should be thrown out long since.

We even have dna sequenced hybrid of neanderthals and moderns that has neanderthal mtdna which is AFTER this bone's age so this alone falsifies this silly hypothesis.

Basically that the Neanderthal admixture had been in the Sardinian/French populations for longer, suggesting that the admixture was older in these populations than for the eastern modern populations. I think the younger ages of the admixture in Han2, Dai2 and Karitiana is due to a second admixture event (<700 generations ago) bringing the average down. As Paabo suggested.

@Annie Mouse, fascinating tidbit. So the Neanderthals that mixed with Sardinian/French ancestors 1319-1732 generations ago were potentially different from the Neanderthals that mixed with Han/Dai/Karitiana 988-696 generations ago.

That's enough of a time gap for some evolutionary changes in Neanderthals. Also potentially involving Neanderthals relocating to marginal/suboptimal habitats to avoid EMH - and adapting to those adverse circumstances.

Similar to the Kalahari Desert Kung we see today in the "The Gods Might Be Crazy." Very marginal environment, tough existence - but they used to live in better areas before the Bantu expansion. Just like Amerinds once lived along the main river systems in much better environments than the cold/arid semi-wastelands they were pushed into by later waves of settlers.

We shouldn't assume the ancestral cultures were the same as the survivors who are just barely hanging on today in adverse circumstances. Same for Neanderthals - adversity facilitates evolutionary change (like more extreme cold/altitude adaptations?).

By comparison the earlier Neanderthals that French/Sardinian ancestors met might have been living a comparatively comfortable life with more lax evolutionary pressures and less time to re-adapt to survive alongside EMH.

"So far as I can tell everything merges at 0.1 cM. I read the Weighted CC data quite differently. Basically that the Neanderthal admixture had been in the Sardinian/French populations for longer, suggesting that the admixture was older in these populations than for the eastern modern populations."

It's Karitiana and Ust-Ishim that merge at 0.1 cM, followed by Han, Dai and then the two Europeans. I guess there's a contradiction/confusion between the generations in the top right corner and the graph itself. The "generations" should really be effective population size (smallest in Ust-Ishim with longest chunks, next smallest in Karitiana, largest in Sardinians). But the graph itself clearly shows the highest correlation between Karitiana and Ust-Ishim sites. Just ignore Paabo's "clock."

This paper on the Anzick toddler's genome (12,500kya) might be relevant to the discussion. I just noticed it and others might also have missed it. It appears the exact date and Clovis status is dodgy. Never-the-less it is at least 10kya in America.

http://www.nature.com/nature/journal/v506/n7487/full/nature13025.html

Basically it suggests that Anzick was most probably an offshoot of North American tribes and ancestral to all South American tribes. It does not IMO say that it was the only ancestor, despite how it is being interpreted in the popular press.

An East Eurasian origin for Anzick is clearly stated. If Anzick is Clovis then Clovis is not Solutrean. There is no significant European affinity.

MA-1 is discussed. It is drift mapped as Western Eurasian, which if true means for Americans to have significant MA1 affinity then it must have entered the Americas via another non-Anzick migration group.

Anzick, Mayan and Karitiana were found to have similar MA1 affinity in the paper suggesting a predivergence (ancestral?) source. But to be honest it all sounded a as if they did not have enough MA-1 to be sure about this. So I am not believing it yet, even if it fits with my own opinions on the matter.

YDNA=Q-L54*(xM3)mDNA=D4h3a

Oldest America habitation dates back ~60kya in Brazil. The Brazilian site at least is going to be a people who predated the arrival of Anzick. Probably Australoids like Luzia. I would love to see DNA for her people. Plus the Dolicocephalics they have been finding in Mexico.

Thanks for letting me know about the paper in your message. It is a good idea, but I believe that the admixture between San and Neanderthal is not recent.

The archaeological evidence suggest that this admixture probably took place either 1) after the San migrated to Europe and founded the Aurignacian civilization;2) when the Neanderthal established settlements in North Africa or 3) before the ancestors of the Neanderthalers Homo heidelbergensis, the European name for Rhodesian man migrated into Europe. If the genetic material came from Homo heidelbergensis , the shared genetic material between San and Neanderthal may have come from an ancestor of Homo heidelbergensis that may have been shared by the first anatomically modern humans in Africa where both hominids lived.

The archaeological research makes it clear Neanderthal probably mixed with Africans. As early as 200kya homo sapien sapiens originated in Africa.

Probably 400-600kya Homo rhodesiensis migrated into Europe. Homo heidelbergensis is the European name for Rhodesian man.

This may be an ancestor of the Neanderthal people (Ki-Zerbo,1981).

The Neanderthal used Mousterian tools. These tools were also being used in Africa as early 130kya. This places Neanderthalers in North Africa.

The human types associated with the Neanderthal tools and recognized by archaeologists as Neanderthal, were found at Jebel Ighoud and Haua Fteah in North Africa. The tools here resemble contemporaneous European neanderthaler tools. The presence of Mousterian tools suggest that Neanderthalers mixed with Africans because we know that anatomically modern humans were living in the area at the time.

Homo rhodesiensis originated in Africa. The ancestor of neanderthal man was Homo rhodesiensis . Between 139kya and 125kya the Neanderthals migrated back into africa and spread from Morocco to East Africa (Ki-Zerbo, 1981,p.572).

The African Neanderthal people used the common Levoiso-Mousterian tool kit originally discovered in Europe. The Nenderthal skeletons mainly come from Djebel Irhoud and El Guettar (Ki-Zerbo,1981). Later Neanderthal people used the Aterian tool kit.

The Neanderthal people were spread from Morocco to the Horn of Africa. This would explain the link between the San and East Africans mentioned in the article you cited.They returned to Africa and introduced the Aterian tool kit.

The graph strikes me as a bit hard to read since it's hard to tell where the colors are overlapping each other. Perhaps it would have been more readable to have separate graphs for each color. It does seem to me that Karitiana is merging at .01 with ust-ishim, though it looks like Han might be as well?

@Grognard

"That makes a huge assumption strands break down at a steady rate which has no merit to it.

If some part of a strand is selected on then it's going to preserve the whole strand until by freak chance the strand breaks. This process is going to be many many times faster with large modern populations than with ancient ones.

Which goes more in line with multiregionalism. If you have already pushed out of africa back so far, it may as well be abandoned. Especially since while the strand sizes are bigger, they don't cotain the same genes that are preserved today."

Agreed on all counts.

@Annie Mouse "The Brazilian site at least is going to be a people who predated the arrival of Anzick."

I don't get why there is so much reluctance to accept continuity between modern and Paleo Indians. There is really nowhere in the world I'm aware of where the oldest skeletons are NOT physiologically quite different from the modern humans residing in that place. Even in Africa, allegedly the origin of humanity, the old "anatomical modern humans" from 100-200 years ago are quite different from the hofmeyr skull (37K yrs ago), which in turn is different than modern African skulls.

"MA-1 is discussed. It is drift mapped as Western Eurasian, which if true means for Americans to have significant MA1 affinity then it must have entered the Americas via another non-Anzick migration group".

Surely that supports the idea that amerindians are a hybrid formed between Western and Eastern Eurasians.

"Oldest America habitation dates back ~60kya in Brazil".

I don't think that is by any means universally accepted. But if true it is extremely unlikely that the Brazilian population has left any descendants today, especially not any haplogroups. They were probably present in unsustainable population numbers.

"I would love to see DNA for her people".

As far as I'm aware no human remains have been found from that period, let alone DNA.

"Why male hybrids may have been sterile - humans have an exceptionally high copy number of TSPY genes"

Unlikely to be the explanation. It is very common that males are sterile in Hybrids between many related mammalian species, not jusy human species. That fact is even mentioned on the video.

"Years ago I saw somewhere that someone was positing that the San were a back-migration from Asia. Can anyone else here chime in on this?"

Dienekes had a post on the subject some months ago. Just enter 'Khoi-San' at the top right of his blog. Maybe without the dash.

Two comments. If Out-of-America were true then the largest amount of Neanderthal and Denisovan admixture should be in modern Africans since they would have had to traverse their territory by the longest path in Asia/Europe to get to Africa. Since that isn’t true, I think we have definitive disproof of Out of America.

I can’t recall ever seeing admixture results of N.’s and D.’s in India. But if Australian Aborigines did take a southerly path to get to Oceania then either Southern Indians were already themselves heavily admixed or the Denisovans were present in Australia/South-East Asia/Oceania and the admixture occurred once they arrived there. In the latter case the race should be on to find Denisovan remains in Australia. The alternative would be that the Australian Aborigines and Papuans took a path down through Siberia to reach Oceania — which seems the most parsimonious suggestion.

Annie Mouse won't be able to support any of her outlandish claims. Anzick is clearly and decisively Amerindian and not East Asians. MA-1 is Amerindian-derived and not East Asian.

@Locrian

" If Out-of-America were true then the largest amount of Neanderthal and Denisovan admixture should be in modern Africans since they would have had to traverse their territory by the longest path in Asia/Europe to get to Africa. Since that isn’t true, I think we have definitive disproof of Out of America."

I'm glad you've disproved something you fail to understand. This is always the easiest route. Africans do have Neandertal and Denisovan alleles, which already means that Africa was colonized from Asia, plus they potentially have a large amount of African "archaic" ancestry, which explains its greater diversity than the diversity of populations outside of Africa. The latter will be impossible to know for sure in the absence of ancient DNA from SS Africa.

@agierung

"The graph strikes me as a bit hard to read since it's hard to tell where the colors are overlapping each other. Perhaps it would have been more readable to have separate graphs for each color. It does seem to me that Karitiana is merging at .01 with ust-ishim, though it looks like Han might be as well?"

I agree the chart is not easy to read. But with or without Han, Karitiana match Ust-Ishim the best. Plus we do have two outstanding Karitiana loci that apparently have the longest Neandertal-like chunk resulting in the absolute highest 0.08 admixture LD coefficient on the Y axis.

"I don't get why there is so much reluctance to accept continuity between modern and Paleo Indians. There is really nowhere in the world I'm aware of where the oldest skeletons are NOT physiologically quite different from the modern humans residing in that place. Even in Africa, allegedly the origin of humanity, the old "anatomical modern humans" from 100-200 years ago are quite different from the hofmeyr skull (37K yrs ago), which in turn is different than modern African skulls."

”Years ago I saw somewhere that someone was positing that the San were a back-migration from Asia. Can anyone else here chime in on this? “

I can’t comment on this but it is interesting to note that the craniometrics and archaeological evidence indicated, to many archaeologists that the Khoisan represented the Cro-Magnon/Grimaldi people who founded the Aurignacian and other early European populations.

There have been numerous "Khoisan skeletons" found in Europe according to Marcellin Boule and Henri Vallois , in Fossil Man (1957). Boule and Vallois reported the find of SSA skeletons at , Grotte des Enfants , Chamblandes in Switzerland , several Ligurian and Lombard tombs of the Metal Ages have also yielded evidences of a Negroid element.

Boule and Vallois (1957), was able to chart the migration of civilization from South Africa to the Aurignacian culture of Europe. These anthropologist reported that the Khoisan shared the same style stone implements and burials 'associated with the Aurignacian or Solutrean type industry...."( Boule and Vallois, 1957, p.318-319). They add, that in relation to Bushman [Khoisan] art " This almost uninterrupted series leads us to regard the African continent as a centre of important migrations which at certain times may have played a great part in the stocking of Southern Europe. Finally, we must not forget that the Grimaldi Negroid skeletons show many points of resemblance with the Bushman [Khoisan] skeletons" (Boule and Vallois,1957).

"But if Australian Aborigines did take a southerly path to get to Oceania then either Southern Indians were already themselves heavily admixed or the Denisovans were present in Australia/South-East Asia/Oceania and the admixture occurred once they arrived there".

The latter seems to be the accepted position, but I fail to see why the obvious isn't considered: the Australian ancestors picked up the Denisova element as they passed through the region where Denisovans have been confirmed as being present. There is no evidence at all that any 'Denisova' element was present from ancient times in SE Asia.

"The alternative would be that the Australian Aborigines and Papuans took a path down through Siberia to reach Oceania — which seems the most parsimonious suggestion".

That was what I have considered the most likely explanation since long before Denisovans were even discovered.

One other thought may help you here. In the 1990s-early 2000s, when people thought that Eurasians didn't admix with Neandertals, geneticists invented the "coastal migration" theory to explain how Eurasians circumvented Neandertals to get to Australia.

While looking out of Africa, the coastal migration theory holds no water, I may be able to recycle its explanatory potential to answer your question how come Africans are not richer in Neandertal and Denisovan genes than the rest of us. I guess they took a coastal route from Asia. In fact, Y-DNA shows that the majority of Africans belong to hg E, which is linked to hg D, and the latter does have a coastal distribution in Asia being found in such places as Japan and Andaman islands.

More research needs to be done on the extent to which Africans have Neanderthal admixture (and the extent to which all humans have Denisovan admixture). That said, It really seems to me that we are dealing with a split between two human populations ~50-60 K (?) years ago: one that was better adapted for a warmer climate, and did NOT interbreed with Neanderthals, and one adapted for a colder climate that did interbreed with Neanderthals. The second group spread all over the world and interbred with the former group and well as other human archaics (e.g. Denisovans and archaic Africans). Amerindians are purely the second group, since there were no other humans/archaic humans in America, while southern Africans are mostly the former. It explains why Africans and Amerindians appear to be the two most "divergent" populations and why the former have far less Neanderthal admixture than the latter. It also explains Amerindian genetic signals in Ma'lta and European hunter gatherers. The question of where and when this split occurred is left open. I guess this would be an Out-of-Africa/Arabia, Out-of-America, and multi-regional hybrid theory, of sorts.

German, to what extent due you think modern Africans are a mix between [paleo] Amerindians and African archaics? Because it seems like it would take a substantial amount of Archaic admixture to dilute the neanderthal component and contribute to high genetic diversity in Africans.

Almost everyone, apart from you, would agree with her [An East Eurasian origin for Anzick is clearly stated].

"the coastal migration theory holds no water"

I agree with you on that. It doesn't make any sense at all, never has.

"the latter [Y-DNA D] does have a coastal distribution in Asia being found in such places as Japan and Andaman islands".

But the link between Japan and the Andamans is overland, not coastal. D is diverse in Tibet and so the most obvious conclusion is that Japan and the Andamans are opposite geographic extremes of its overland expansion. That rather negates the idea that E's arrival in Africa was via a southern coastal migration.

Not only that but there appear to be a number of north American skulls/bones that do not appear to strongly resemble the modern Amerindian population. The following site has a strong agenda/bias, and not all the stuff is beleiveable. But check out the map of the USA showing skulls marked "X". No similarity to modern American Indians.

"German, to what extent due you think modern Africans are a mix between [paleo] Amerindians and African archaics? Because it seems like it would take a substantial amount of Archaic admixture to dilute the neanderthal component and contribute to high genetic diversity in Africans."

Yes, this seems to be the situation. Ironically, Out-of-Africa has construed Africans as genetically essentially 100% archaic. They are black because they've always been exposed to African UV light. Their lineages are 200,000 years old when there were no modern human toolkits around. Then a severe bottleneck (only 2 mtDNA lineages out of several dozens) associated with a symbolic revolution around 50,000 YA finally resulted in a small group of Africans to escape the Neandertal hold, colonize the world and lose their dark pigmentation. Amerindians, on the other hand, have always been construed as an evolutionary dead-end, an offshoot of East Asians that lost most of the modern diversity accrued outside of Africa.

Out of America reverses this: Amerindians are not a dead-end but a relatively pure and demographically depressed leave-behind from the modern human speciation event, while Africans are an offshoot of a fully modern, Asian-derived population that experienced a strong influx of "archaic" genes in Africa. If you look at Y-DNA hg E is a large, pan-African haplogroup which represents an out-of-Asia migration, while hgs A and B are localized and rare traces of an archaic substrate. It's ironic that people think that Amerindians come from East Asians, while in reality it's Africans who came from (East) Asians. Khoisans still have lighter skin, epicanthus and elevated frequencies of dental shoveling.

@Ryan

"It doesn't seem like very good science if you accept or reject coastal migration based on whether or not it supports your Out-of-America hypothesis."

Wrong address! The coastal migration hypothesis was an ad hoc idea created by geneticists to justify out of Africa with no Neandertal admixture. I'm just showing how woefully misguided scientists are - not only that they missed critical data, but the hypothesis itself can easily be hijacked to illustrate a completely opposite scenario.

”German, to what extent due you think modern Africans are a mix between [paleo] Amerindians and African archaics? Because it seems like it would take a substantial amount of Archaic admixture to dilute the neanderthal component and contribute to high genetic diversity in Africans.”

This question can not be answered because contemporary Amerindians are not related to Paleo-Amerindians. Neves made it clear that Luzia for example could have been Australian or African. The Paleo-Ameridians could have been African since Africa is closer to South America than Australia. The recent paper by Gundula Povysil, Sepp Hochreiter make the idea that Africans and Neanderthals fail to exhibit any relationship mute, they wrote “This hints at a gene flow from Neandertals into ancestors of Asians and Europeans after they left Africa. Interestingly, many Neandertal- or Denisova-matching IBD segments are predominantly observed in Africans - some of them even exclusively. IBD segments shared between Africans and Neandertals or Denisovans are strikingly short, therefore we assume that they are very old. This may indicate that these segments stem from ancestors of humans, Neandertals, and Denisovans and have survived in Africans.”

"German, to what extent due you think modern Africans are a mix between [paleo] Amerindians and African archaics?"

German has always carefully avoided that topic. He is forced to admit that any 'out of America' population must have mixed with other populations in Eurasia to explain the great divergence between East and West Eurasians. Consequently by the time any OoAmerica population arrived anywhere near Africa the African element would have become greatly diluted. Thus destroying any meaningful out of America scenario.

"Nothing from as far back as 60k. But Luzia is a skeleton".

But I was meaning specifically the absence of ancient skeletal material.

"there appear to be a number of north American skulls/bones that do not appear to strongly resemble the modern Amerindian population".

I fully accept the earliest Americans are far less 'Mongoloid' than are later ones. This probably reflects a higher proportion of MA-1 type genes in the earlier groups, followed by a higher 'East Asian' proportion in later arrivals. Of course german sees things differently but can't really explain the difference between 'early' and 'later'.

"This question can not be answered because contemporary Amerindians are not related to Paleo-Amerindians. Neves made it clear that Luzia for example could have been Australian or African."

No. They are all the same genetically (http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0005746), so what Neves has uncovered is high phenotypical variability stemming from the same (old, I'd add) genetic base.

What absolute rubbish! Out of Africa posits that sapiens began in Africa some 200kya ago, well before the Out of Africa event, and "archaics" are populations that had already diverged before this point. You are just making up your own definition of "archaic" and attempting to apply it where it doesn't fit.

One pattern I've noticed with you German is that you regularly preface your irrationality by falsely accusing others of exactly what you are about to do yourself - you often call people "biased" for no valid reason and then give a completely one-sided interpretation, and multiple times you've falsely labelled me a "science-denier" and then proceeded to deny the science yourself, sometimes in the very next sentence! Since you just tried to imply that Out of Africa is inherently racist, that means you're about to say something like ...?

Africans are an offshoot of a fully modern, Asian-derived population that experienced a strong influx of "archaic" genes in Africa

... and there it is! Given that African diversity is greater than all non-African diversity put together, this means that under your theory Africans would have to be less than 50% homo sapiens! Are you saying that Africans are sub-human? Really? Are we living in the 50s?

At any rate this certainly throws some light on why you repeatedly refer to Native Americans as a "pure" population - your theory is looking less and less like science and more like some sort of "Amerindian-supremacist" crusade. Whatever Carlos Castaneda and Dances With Wolves led you to believe, you're just going to have to accept that Native Americans are normal humans just like the rest of us (including Africans!)

"What absolute rubbish! Out of Africa posits that sapiens began in Africa some 200kya ago, well before the Out of Africa event, and "archaics" are populations that had already diverged before this point. You are just making up your own definition of "archaic" and attempting to apply it where it doesn't fit."

You are absolutely unfamiliar with anthropology, or discourse analysis or any those disciplines, hence you're throwing another hysterical fit because your cosmological views are being shattered by evidence. As I have already explained to you, there are things that people say overtly (calling Africans "modern") and then there's an unstated logical outcome of the theory. In the out-of-Africa framework, Africans are of course referred to as "modern" (that's where supposedly "biological modernity" started), but in essence they are being portrayed as "archaic," while true modernity (sometimes referred to as "behavioral modernity" attested globally from 50,000 years on) is construed as an evolutionary advantage that enabled modern humans to leave Africa, replace Neandertals and colonize the world. The way mtDNA trees were constructed is that they show layers of African-specific lineages (derived ultimately from an extinct "archaic" population) of which non-Africans are a small subset. So, effectively modern Africans are closer to extinct archaics genetically, while modern non-Africans are further removed from archaics because they are immediately derived from most recent African lineages. The fact that all lineages attested in modern Africans were originally interpreted as automatically African native lineages (not lineages derived from an archaic substrate through admixture), while all the "archaic" lineages were thought of as extinct in Africa made Africans effectively the only surviving archaic population, while non-Africans who were enabled with "behavioral modernity" and went through a bottleneck as they left Africa the only true modern humans.

If from the very beginning certain lineages found in modern Africans were interpreted as "introgressed," while certain others as "modern." This problem wouldn't have existed. Out-of-America puts logic back into human origins theorizing by showing that only those African lineages most closely related to non-African lineages (e.g., Y-DNA E, mtDNA L3) can qualify as modern human lineages. They are most widely spread and most frequent in Africa, but all others are the molecular survivals of those "archaic" populations that went extinct.

"One pattern I've noticed with you German is that you regularly preface your irrationality by falsely accusing others of exactly what you are about to do yourself - you often call people "biased" for no valid reason and then give a completely one-sided interpretation, and multiple times you've falsely labelled me a "science-denier" and then proceeded to deny the science yourself, sometimes in the very next sentence!"

The "pattern" that you see is the product of your imagination.

"Since you just tried to imply that Out of Africa is inherently racist, that means you're about to say something like ...?"

I personally don't say this because I know very well the people who are behind population genetics in the U.S. and Russia but a lot of people in and outside of academia think of genetic studies as "new racism." I'm just trying to fix the problem, so that honest scientists don't have to suffer from a critique that should be addressed at the inherited "cultural baggage" that these geneticists have to work within, not at them personally.

"Are you saying that Africans are sub-human? Really? Are we living in the 50s? "

Well, you definitely are. In the 1850s. There's no conversation about anybody's subhumanity. It increasingly looks like that the "human family" began with heidelbergensis and not with sapiens. But it's useful to maintain "modern" vs. "archaic" to differentiate between living (Homo sapiens) and extinct (Neandertals, Denisovans, African archaics, etc.) human populations, so that we correctly identify the original homeland of the former and the later admixtures of the former with the latter.

"ike some sort of "Amerindian-supremacist" crusade. Whatever Carlos Castaneda and Dances With Wolves led you to believe."

I definitely don't believe that Amerindians is an evolutionary dead-end - a cultural notion that made the colonization and the depopulation of the Americas easier on our collective conscience. As for Carlos Castaneda and Dances with Wolves, these are not my favorite book and movie. If you want to understand my intellectual roots, read Tolstoy and Dostoevsky and watch One Flew Over the Cuckoos Nest. I do feel like McMurphy among crazies when I talk to you, Terry and some others...

Thanks for the article. This paper does not really prove that the ancient skeleton(s) from Brazil, i.e., Luzia , carry the same genes as contemporary Amerindians. The sample in this study came from Argentina. The dates assigned to the sample range between 6,000-10,000 years later than Luzia. Given the difference in dating of these skeletons they can not be used to claim the archaic Indians carried the same genes as contemporary Amerindians.

The South American founder population could have changed during this period.In 6,000 years migrants crossing the Beringa would have made there way to South America. Look at how in less than 500 years the vast majority of Americans today are craniometrically European, instead of Amerindian.

The presence of mtDNA haplogroup A among Native Americans does not mean Africans may have been representatives of the population from which Luzia originated. Haplogroup A is found among Mixe and Mixtecs (4).

The mtDNA A haplogroup common to Mexicans is also found among the Mande speaking people and some East Africans (4-6).The Mande speakers carry mtDNA haplogroup A, which is common among Mexicans (6). In addition to the Mande speaking people of West Africa, Southeast Africa Africans also carry mtDNA haplogroup A (5).

I always gathered that the appeal of Out-of-Africa for at least some of its proponents is that it made all of humanity seem united in one "type" that only emerged 45-60K years ago. It serves the purpose of minimizing differences between modern populations. Of course one of the side effects of this idea was the de-humanization of archaics like Neanderthals. Not to mention the endless search for what modern Africans preserve the most 'archaic" human lineages (which I guess is what German was alluding to).

@German

" It increasingly looks like that the "human family" began with heidelbergensis and not with sapiens. But it's useful to maintain "modern" vs. "archaic" to differentiate between living (Homo sapiens) and extinct (Neandertals, Denisovans, African archaics, etc.) human populations, so that we correctly identify the original homeland of the former and the later admixtures of the former with the latter."

I think this is an important point. It's better to talk about "moderns" and "archaics" as separate populations, that all fall under the umbrella "human", rather than seperate species.

@ Dr. Clyde

"This paper does not really prove that the ancient skeleton(s) from Brazil, i.e., Luzia , carry the same genes as contemporary Amerindians. The sample in this study came from Argentina. The dates assigned to the sample range between 6,000-10,000 years later than Luzia. Given the difference in dating of these skeletons they can not be used to claim the archaic Indians carried the same genes as contemporary Amerindians."

It's true, the paper doesn't have DNA for Luzia or other comparably old remains. However, what the paper demonstrates is that there can be craniometric variation EVEN IN populations with similar mtDNA profiles. Hence, we need to be cautious about attributing craniometric differences to differences in ancestry.

@German:Africans are of course referred to as "modern" (that's where supposedly "biological modernity" started), but in essence they are being portrayed as "archaic,"

What are you talking about German? Africans have music, art, tools, language, fire, mining, metallurgy and every other kind of behavioural modernity we see in non-African groups. Your view of African culture as more primitive than non-African culture is the only "archaic" thing here.

So, effectively modern Africans are closer to extinct archaics genetically, while modern non-Africans are further removed from archaics because they are immediately derived from most recent African lineages.

All African lineages were the same age at the OOA event. The lineages that remained in Africa are just as "recent" as the one that non-Africans derived from. Non-Africans are closer to the archaics we know about (Neanderthals and Denisovans) than Africans are. "Effectively" you are just making things up with no evidence again.

The "pattern" that you see is the product of your imagination.

Most certainly, but you *are* trying to make out that OOAfrica is inherently racist and thus making the racist conclusion of your own theory more palatable... so maybe my imagination and reality aren't so different in this case.

I definitely don't believe that Amerindians is an evolutionary dead-end

"This paper does not really prove that the ancient skeleton(s) from Brazil, i.e., Luzia , carry the same genes as contemporary Amerindians. The sample in this study came from Argentina."

The paper says: "The oldest samples from the region under study, dated on ca. 8,000–2,000 years BP, present more elongated crania than the Later Late Holocene samples, but both groups have the same mtDNA haplogroups (and even haplotypes)."

Although more research is needed and we indeed don't have DNA from Lagoa Santa, but as of now this disproves your broad claim that "contemporary Amerindians are not related to Paleo-Amerindians."

German Dziebel ,Excellent summary of the “unstated logical outcome” of the Out of Africa theory, what I have referred to when discussing the subject with die hard OOA true believers as the “unstated implications” of the theory. These discussions usually degenerate into the OOA supporter reciting common talking points of the theory while they simultaneously refuse to discuss any evidence which may, as you put it, “shatter their cosmological views”. It is refreshing to hear someone drawing the inescapable logical conclusions of the OOA theory. I am quite intrigued by your “Out of America” theory but do not have enough information about it to draw a clear picture. Would you be able to elaborate or refer me to a source for more information? Thank you in advance.

"Although I am not sure that the earliest arrivals will be entirely MA-1 -esque".

I agree. The earliest arrivals already had more East Asian element than did MA-1.

@ Dr. Clyde Winters:

"The mtDNA A haplogroup common to Mexicans is also found among the Mande speaking people and some East Africans (4-6).The Mande speakers carry mtDNA haplogroup A"

I have certainly never heard that, and I see no mention of it in the references you list. Y-DNA certainly. Do you have a specific reference?

@ German:

"true modernity (sometimes referred to as 'behavioral modernity' attested globally from 50,000 years on) is construed as an evolutionary advantage that enabled modern humans to leave Africa, replace Neandertals and colonize the world".

Am amzing comment from someone who had just written:

"You are absolutely unfamiliar with anthropology, or discourse analysis or any those disciplines"

That last statement was obviously written by someone with no knowledge of evolutionary biology whatsoever, or even anthropology although I know you'll disgree with me on that. The change to 'behavioral modernity' of 50,000 years ago is these days not considered to be what let humans emerge from Africa. The idea was always more popular with the masses rather than amoung scientists anyway. It is now blindingly obvious that modern humans emerged from Africa before the suite of cultural (rather than biological) changes that gave rise to what we now call the Upper Paleolithic. In fact it has always been obviously so because Australian Aborigines did not have an Upper Paleolithic culture, yet few would dare call them other than genetically modern humans. The remainder of your comments concerning Africans I consider to be the product of your racism.

"What are you talking about German? Africans have music, art, tools, language, fire, mining, metallurgy and every other kind of behavioural modernity we see in non-African groups. Your view of African culture as more primitive than non-African culture is the only "archaic" thing here."

Khoisan clicks are interpreted as archaic human sounds lost in all other languages (http://www.cell.com/current-biology/abstract/S0960-9822(03)00130-1?switch=standard). Khoisan and Pygmy music is interpreted as archaic and progressively lost as humans colonized areas outside of Africa (http://soundingthedepths.blogspot.com/). It's the same logic as with Africans' dark pigmentation: an archaic trait lost in populations outside of Africa.

You are willing to debate every point but you invariably lose every battle, whether it's about anthropology, linguistics, musicology, genetics, mathematics. A typical creationist behavior. Can you adopt science for a little while and give yourself a break?

"All African lineages were the same age at the OOA event."

Geneticists derive non-African lineages M and N from an African-specific node L3, which is in turn derived from a deeper African node, L3'4'5'6 (or something like that, it varies a bit), which in turn derives from an even deeper African specific node L2'3'4'5'6, which in turn derives derives from a still deeper African specific node L1'2'3'4'5'6, which derives from the deepest African specific node L1'2'3'4'5'6. Obviously, M and N are separated from L1'2'3'4'5'6 by layers and layers of African-specific nodes. Hence, non-Africans are portrayed as more removed from archaic Africans than modern Africans are.

"Most certainly, but you *are* trying to make out that OOAfrica is inherently racist and thus making the racist conclusion of your own theory more palatable... so maybe my imagination and reality aren't so different in this case."

I personally don't care if out-of-Africa or any other theory is racist or not, but objectively there are no reasons to conclude that out-of-Africa is a decisive break from racist thinking. (This is where Cavalli, Mountain and others are rather naive but I never attempted to dissuade Joanna from thinking this way because I don't like politics.) Out-of-America is the only antidote to racism, new, old, imaginary, real, or any other. It places the origin of modern humanity on a continent devoid of archaic hominins and it interprets archaic traits in Old World populations as coming from admixture, not from common descent (unlike out-of-Africa and Multiregional).

"Who does? I've never heard this idea from anybody but you."

Well, compare two ideas: one postulates that America was peopled from Asia 12,000 years ago and lost most of the genetic diversity accrued over the previous 190,000 years. (Not counting all the genetic diversity lost by Amerindians since 1492.) The other one postulates America as the source. Once the second one is put on the table, the first one becomes a "dead-end" theory of Amerindian origins. You need to get more savvy when you read academic literature.

"Well you certainly seem to have a similar moral compass to him."

Excuse me? I'm the one who valiantly fights against obscurantism and biases. Your "judgment compass" in out of whack.

"Geneticists derive non-African lineages M and N from an African-specific node L3, which is in turn derived from a deeper African node, L3'4'5'6 (or something like that, it varies a bit), which in turn derives from an even deeper African specific node L2'3'4'5'6, which in turn derives derives from a still deeper African specific node L1'2'3'4'5'6, which derives from the deepest African specific node L1'2'3'4'5'6. Obviously, M and N are separated from L1'2'3'4'5'6 by layers and layers of African-specific nodes".

Wow. You finally can see that M and N derive from Africa. It all sounds like 'out of Africa' to me. In fact your list is part of the supporting evidence for out of Africa. Where does out of America fit into all that?

"Out-of-America is the only antidote to racism, new, old, imaginary, real, or any other. It places the origin of modern humanity on a continent devoid of archaic hominins"

'Devoid of archaic hominins'? How on earth do you twist that to become 'out of America'? Surely there is no other option than that Amerindians formed from some sort of modern humans who entered that double continent at some time. Where does out of America fit into all that?

"Hence, non-Africans are portrayed as more removed from archaic Africans than modern Africans are".

And what makes you believe that the earlier, specifically African, haplogroups were not carried by thoroughly modern humans? Genetics involves far more than just mt-DNA haplogroups but, not being a geneticist, you wouldn't know that.

"compare two ideas: one postulates that America was peopled from Asia 12,000 years ago and lost most of the genetic diversity accrued over the previous 190,000 years".

There you go again. This time it is population genetics you don't understand. How would any population, no matter how numerous, be able to carry every single genetic variation from across the whole world into America? As I said yesterday, 'The one thing spectacularly missing from Out-of-America is logic'.

"The other one postulates America as the source".

With no evidence for it at all except for some shonkey idea about the survival of primitive social systems.

@CleverPrimate:Excellent summary of the “unstated logical outcome” of the Out of Africa theory

I suggest you look at the logic a bit deeper - what German has done is take a term related to genetics ("archaic" - meaning diverged before the evolution of homo sapiens c. 200kya) and associated it as the opposite of a term related to culture (ie "non-modern" - meaning before the UP revolution c50kya). It's a semantic trick to get you to associated unrelated concepts as if they are the same. There's no logical connection between the behavioural characteristics of a population at 50kya and their ancestor's genetic disposition at 200kya, despite what German's verbal gymnastics may be trying to imply.

@German:Khoisan clicks are interpreted as archaic...

The ref says "ancient" - this does not correlate with genetically "archaic".

Khoisan and Pygmy music is interpreted as archaic

The blog doesn't use "archaic" in this context - it posits a "Hypothetic Baseline Culture" of roughly 60-100kya ago, well after the divergence of sapiens and the archaics. The author explicitly states "it is important to understand that the Pygmies and Bushmen of today may, on the whole, be no more similar to the common ancestors than any other indigenous groups, hunter-gatherers or otherwise. They are most certainly not 'stone age' relics or 'living fossils.'"... clearly contradicting what you are trying to imply with your use of the term "archaic".

It's the same logic as with Africans' dark pigmentation: an archaic trait lost in populations outside of Africa.

It's an "ancestral" trait, not "archaic". Furthermore dark pigmentation is widespread outside Africa, and if the LB/Loschbour samples are representative was even widespread throughout Europe until very, very recently.

Obviously, M and N are separated from L1'2'3'4'5'6 by layers and layers of African-specific nodes. Hence, non-Africans are portrayed as more removed from archaic Africans than modern Africans are.

You're just counting identified haplogroups between the modern and basal lineages, and assuming that this represents age or distance. It doesn't. All modern populations are the same distance from their MCRA - by definition. There may be more signposts identified on one path over another, but that doesn't change the net distance of each path - they just draw it like that on the pretty pictures so they can fit them all in.

Out-of-America is the only antidote to racism

Yes German, it's the holy shining light is a sea of depravity.

The racism inherent the OOAm theory you've presented is that it posits the high genetic diversity in Africa is solely due to non-sapiens admixture. Since this diversity is relatively homogenous and is greater than all the diversity in non-Africans, it requires that modern Africans have a majority non-sapiens DNA... something the Ku Klux Klan will no doubt be very happy to agree with.

one postulates that America was peopled from Asia 12,000 years ago and lost most of the genetic diversity accrued over the previous 190,000 years

Amerindians kept a great deal of the East Asian diversity, and have been evolving their own unique diversity ever since. There's no "dead end" here, it's just your personal prejudices showing through.

I'm the one who valiantly fights

"Valiant" implies honour. Personal insults, misrepresentation of data, denial of established science, semantic trickery... none of these inspire the word "valiant" to me, but hey, be your own judge.

I can access only the abstracts of the articles you mention. I would guess that any mt-DNA A in Africa would be the product of a slave dealers American wife. Haplogroup A in Africa would be completely surprising. I googled 'mitochondrial dna haplogroup a mande'. No mention of A anywhere in Africa, except Y-DNA A of course. Can you provide more specific information?

“Out-of-America is the only antidote to racism, new, old, imaginary, real, or any other. It places the origin of modern humanity on a continent devoid of archaic hominins and it interprets archaic traits in Old World populations as coming from admixture, not from common descent (unlike out-of-Africa and Multiregional). “

This is plainly absurd. Whatever place you pick for the origin of modern humans they have to have evolved from more archaic forms. So if America *were* the origin of homo sapiens then there would have to be archaic forms in America. Anything else would just be some bizarre form of Creationism.

German, I am done reading your posts. I don’t post much but up to now I have read every post on every thread. But increasingly all rational discussion is being derailed in your ridiculous OoAmerica claims. I can see that you probably formulated this hypothesis before there was any DNA evidence to say anything one way or another, and now you feel obliged, out of a misguided sense of entitlement, to defend it even when the evidence is completely against you. And you like to embellish your empty claims with liberal doses of put-downs and insults for anyone who tries to treat you as a rational human being, subject to the ordinary logic of evidence and inference. It is a disgrace. Academic discourse cannot proceed when someone is willing to twist all the evidence to suit them. And despite your claims to academic credentials and academic legitimacy what I see is merely an internet crank, attempting to make disciples out of the gullible.

So from now on I won’t bother to read the nonsense you are posting. Life is too short. I have lost count of the evidence you are misrepresenting. And I doubt somehow that American Indians will thank you for your efforts to make them the UR-population of a fictionalised Earth.

"I posted photos of the specific sections of the articles that talked about mtDNA haplogroup A on my blog"

Thanks. I see only one listing of mt-DNA A2 in one Mande individual. The others are either Y-DNA or make no mention of mt-DNA A in the list. I still think the most likely explanation is a slaver's Amerindian wife.

@ Locrian:

"This is plainly absurd".

I'm sorry you took so long to realise that about German. I agree completely with your assessment of course. You raise points I hadn't even thought of.

"The ref says "ancient" - this does not correlate with genetically "archaic"."

Here and below you're ignoring the distinction between what's explicitly stated in a theory and what's a necessary logical outcome of a theory. Africans are routinely presented as "archaic" and non-Africans as "modern." But the way academic scientists who support out-of-Africa talk about it as "ancestral" vs. "derived," and they create caveats that "ancestral" doesn't mean "archaic." But ancestral IS archaic and derived IS modern, and the rest is their wishful thinking. If all "archaic" populations vanished and the only split that's being postulated is between "Africans" and "non-Africans," Africans are the only surviving archaics and non-Africans are derived from them through a massive bottleneck, hence modern. This is what Darwinism would require. Unless of course, Africans were created by God (well, maybe the use of Adam and Eve by geneticists is more than a metaphor....)

"despite what German's verbal gymnastics may be trying to imply."

I'm correcting academic scientists' verbal gymnastics and lack of logic. Don't put the blame on the mirror if the face is ugly.

"Furthermore dark pigmentation is widespread outside Africa, and if the LB/Loschbour samples are representative was even widespread throughout Europe until very, very recently."

Sure, but extremely dark pigmentation of Africans is routinely used as evidence of their long tenure in those latitudes.

"You're just counting identified haplogroups between the modern and basal lineages, and assuming that this represents age or distance. It doesn't. All modern populations are the same distance from their MCRA - by definition. There may be more signposts identified on one path over another, but that doesn't change the net distance of each path - they just draw it like that on the pretty pictures so they can fit them all in."

So, genetic distances don't exist?

"The racism inherent the OOAm theory you've presented is that it posits the high genetic diversity in Africa is solely due to non-sapiens admixture. Since this diversity is relatively homogenous and is greater than all the diversity in non-Africans, it requires that modern Africans have a majority non-sapiens DNA... something the Ku Klux Klan will no doubt be very happy to agree with."

Yes, let's choose a scientific theory that would keep KKK unhappy. I never said that extinct Africans with whom Asians mixed were "non-sapient." We don't know that, they went extinct.

"Amerindians kept a great deal of the East Asian diversity, and have been evolving their own unique diversity ever since.'

Just keep selling me your baloney, Tobus. In a different string, you are all over the idea that Amerindians went through a massive bottleneck that resulted in the loss of most of East Asian and West Eurasian diversity and made their heterozygosity similar to that of Denisovans and Neandertals.

""Valiant" implies honour. Personal insults, misrepresentation of data, denial of established science, semantic trickery... none of these inspire the word "valiant" to me, but hey, be your own judge."

I haven't misrepresented any data or engaged in semantic trickery. Personal insults is just a matter-of-fact talk when it comes to rabid pseudoscientists and unethical debaters such like yourself. I do question the academic consensus. This is a good thing, I think.

"So from now on I won’t bother to read the nonsense you are posting. Life is too short. "

Thank you for pulling out. The last thing I need is another anonymous blogger who contributes nothing to science and wastes my time telling me that there turtles all the way down. Out-of-Africa is a perfect intellectual abode for people like you.

Africans have more derived alleles than the rest of the world put together, so that should make them the most "modern" by your reckoning. You are repeating a whole hash of outdated nonsense that disappeared from the scientific mainstream 20 years ago - perhaps it's time to update your understanding of African genetics and culture.

you are all over the idea that Amerindians went through a massive bottleneck that resulted in the loss of most of East Asian and West Eurasian diversity and made their heterozygosity similar to that of Denisovans and Neandertals.

By what stretch of the imagination are you saying that Amerindian heterozygosity is "similar" to that of Denisovans and Neanderthals? Prufer clearly shows that Amerindian heterozygosity is much more similar to that of East Asians, Papuans and other Eurasians than to the archaics. So while the bottleneck certainly lowered Amerindian genetic diversity, it didn't obliterate it to anywhere near the levels seen in the archaics.

I haven't misrepresented any data or engaged in semantic trickery.

You have multiple times, such as just above when you said that Amerindian heterozygosity is "similar to that of Denisovans and Neanderthals". It's not similar to them at all (60k cf 25k). You got to that ridiculous misrepresentation by overstating your semantic trick of implying "closest" means "close". And we've already been through how you used "non-modern" (pre 50kya) to imply "archaic" (pre 200kya). I could go on...

Personal insults is just a matter-of-fact talk when it comes to rabid pseudoscientists and unethical debaters such like yourself.

No.. it's just being a jerk. Insults have no place in intelligent discussion, particularly when they are used in lieu of evidence and reasoning.

I do question the academic consensus. This is a good thing, I think.

It is, but only if you have some genuine reason to do so... fabricating "facts" in the face of overwhelming evidence just so you can challenge the consensus is not a good thing... sometimes the consensus is the consensus for a reason.

"By what stretch of the imagination are you saying that Amerindian heterozygosity is "similar" to that of Denisovans and Neanderthals?"

Look at the latest Lazaridis's Table S2.2. Amerindians are closer to Denisovans than they are to Africans. The heterozygosity differences are smoother between Amerindians, Papuans, Asians and West Eurasians, and we shouldn't split hairs about it, but the difference between Karitiana A and Denisovans is roughly the same as between Karitiana A and French or Shtuttgart. When you (and others) postulate the mixture of East Asians and West Eurasians to generate Amerindians, you completely overlook the fact that this scenario can't possibly account for the low heterozygosity of Amerindians. Defensively, you resort to an opposite scenario, namely a bottleneck, which kicked in after the admixture to reduce this hypothetical elevated heterozygosity to almost Denisovan level. This is just nonsense.

"Africans have more derived alleles than the rest of the world put together, so that should make them the most "modern" by your reckoning. You are repeating a whole hash of outdated nonsense that disappeared from the scientific mainstream 20 years ago - perhaps it's time to update your understanding of African genetics and culture."

There are several centuries of difference between your pre-1492 vision of the world and mine. The proportion of derived vs. ancestral alleles varies from locus or locus and we don't have a full view of it yet on a continent by continent level. But what's your reference for your claim in the first place? Tobus & Tobus Consulting, Inc.?

"You have multiple times, such as just above when you said that Amerindian heterozygosity is "similar to that of Denisovans and Neanderthals". It's not similar to them at all (60k cf 25k). You got to that ridiculous misrepresentation by overstating your semantic trick of implying "closest" means "close"."

You just don't know the data and don't understand English well. Out of all modern human populations, Amerindians are the closest to Neandertals and Denisovans in terms of their demographic/genetic structure. Even more so, as the Lazaridis's table indicates, they are closer to them than to Africans.

"And we've already been through how you used "non-modern" (pre 50kya) to imply "archaic" (pre 200kya). I could go on..."

This is not my awkward language, it's academic scientists' parlance. And its confusing. But your fault was to venture a ridiculous accusation that my model of the peopling of Africa makes them look "pre-sapient." And it's a proven fact that Africans are portrayed as carrying "archaic" features of phenotype, language, music, etc. If people don't directly attribute them to the so-called "AMH" in Africa doesn't make the outcome different.

"No.. it's just being a jerk. Insults have no place in intelligent discussion, particularly when they are used in lieu of evidence and reasoning."

Everything that you subjectively and defensively present as "personal insults" are just facts about you as an anonymous (already unethical at that), ignorant blogger who tries to defend his beliefs without using facts and attacking an honest, well-credentialized scientist for unorthodox but rigorous thinking. You deny science and you deny my scientific credentials. This is a sad pattern and I didn't get you there. You got to this place yourself.

"It is, but only if you have some genuine reason to do so... fabricating "facts" in the face of overwhelming evidence just so you can challenge the consensus is not a good thing... sometimes the consensus is the consensus for a reason."

A creationist like you of course believes that a consensus is based on a revelation or "reason" of sorts. The reality is there's no reason for a scientific consensus, and the "consensus" in the field of human origins has been in flux for the past 10 years, even without me rocking the boat. I never fabricate facts but I do bring to light the facts that consensus-huggers such as yourself tend to sweep under the carpet. And this is a huge difference that puts you outside of science.

@German:a bottleneck, which kicked in after the admixture to reduce this hypothetical elevated heterozygosity to almost Denisovan level. This is just nonsense.

The only nonsense here is "almost Denisovan level". Low as it is Amerindian heterozygosity is still about 3 times higher than Denisovans', and is a little more than half of Africans'... so saying Amerindian heterozygosity is "almost Denisovan" is absolute codswallop (to phrase it nicely).

But what's your reference for your claim in the first place?

It's a logical consequence of high heterozygosity - you can't have high heterozygosity unless you have a high number of derived alleles (think about it!) It's confirmed by the high number of African private alleles (Tishkoff) and by the high number of African-only SNPs in various panels (such as in Patterson 2012).

Out of all modern human populations, Amerindians are the closest to Neandertals and Denisovans in terms of their demographic/genetic structure.

But "closest" (or "most similar") doesn't always mean "close" (or "similar") - the number 60 is "closest" to 25 out of 60, 70 and 80, but that doesn't make it "close" to 25. Amerindian and Denisovan demographic/genetic structure are not at all similar. You started out using (technically) correct phrases like "most similar" and "closest to" to imply a correlation, and now you are going beyond this and saying they effectively *are* the same with phrases like "almost Denisovan", "is similar to" and "as homozygous as". This is a intentional misrepresentation of the data through deliberate semantic trickery.

As it turns out Loschbour has lower heterozygosity than Amerindians anyway, so your point is moot... unless you now believe we all came from European hunter-gatherers?

This is not my awkward language, it's academic scientists' parlance. And its confusing.

Well it didn't confuse me. "Archaic" in a genetic sense refers to pre-sapiens lineages. It was very clear that none of the sources you brought were talking about pre-sapiens populations, and none of them use the word "archaic" anyway, so I find it very hard to believe you were just "confused" and not deliberately trying to present something not supported by the sources.

But your fault was to venture a ridiculous accusation that my model of the peopling of Africa makes them look "pre-sapient."

.. and yet you still haven't explained how your theory that all African diversity can be attested to pre-sapiens admixture does not logically require that Africans be primarily non-sapiens. It seems to be a reasonable conclusion given the presumptions of your theory provided so far.

Everything that you subjectively and defensively present as "personal insults" are just facts

If I were fat, bald and ugly too would that make you less of a jerk if you pointed it out? If you have logically consistent reasoning and verifiable facts then present them - nobody's going to change their mind just because you called them names, factual or not (and if you think "bible-basher", "creationist bigot" and "consensus-hugger" are facts, then I suggest you get a better dictionary)

You deny science and you deny my scientific credentials.

I've never denied the science, just your personal interpretation of it, and your "scientific" credentials don't mean you are always right - you still need to use facts and logical reasoning to back up your interpretations.

I never fabricate facts

*Ahem* You JUST fabricated that Amerindian heterozygosity is "almost Denisovan level", and previously that it is "similar to that of Denisovans and Neanderthals" and on another thread that Amerindians are "as homozygous as Denisovans". None of these "facts" are true.

"With the exception ofone sequence (H001) belonging to the east Asian/NativeAmerican haplogroup A (which exactly matches one individualfrom the Brazilian sample of Alves-Silva et al.2000), all southeastern African sequence types could beclassified as L-types".

The authors make no attempt to explain its presence but I still think it's likely to be a slaver's girlfriend. I'd be very surprised if the men who moved back and forth between Africa and America never took any women with them.

@ German:

"the 'consensus' in the field of human origins has been in flux for the past 10 years"

As usual for you that statement is absolute rubbish. I started writing my thoughts down concerning human evolution nearly 10 years ago and, looking back, I would change very little. The main thing that has changed is a finer resolution of haplogroups. And this has confirmed many of my suspicions from the time. But of course that is the very improvement in the science that turns you into a fundamentalist creationist. You can't afford to accept haploid phylogenies because they absolutely prove your belief to be wrong. If you really want to read the adjustments I made to what I originally wrote I can provide a link. But, of course, the last thing you will be prepared to do is to admit you have been wrong. Typical of a creationist fundamentalist.

"Also slave traders did not take there wives to Africa. Moreover, American slave traders did not marry Indians".

Sailors at the time certainly did have wives, and sometimes took them home. This old documentary shows one individual who had a Maori' father and a European mother found his mother had previously unknown American ancestry:

http://www.nzonscreen.com/title/made-in-taiwan-2006

The conclusion was that at some time a sailor from England had taken an American wife who had Indian ancestry. Perhaps not Indian herself. Something similar may explain the sporadic mt-DNA As in Africa. It is certainly most unlikely that A's movement was from Africa to America.

"Sailors at the time certainly did have wives, and sometimes took them home. This old documentary shows one individual who had a Maori' father and a European mother found his mother had previously unknown American ancestry:

http://www.nzonscreen.com/title/made-in-taiwan-2006"

I looked at the video they said she was of East Asian origin.

The presence of the A haplogroup among Mande speakers and Southeast Africans who live 1000's of miles away from each other would indicate that Africans carry this haplogroup.

"The presence of the A haplogroup among Mande speakers and Southeast Africans who live 1000's of miles away from each other would indicate that Africans carry this haplogroup".

The presence of a single individual in each of East and West Africa carry the haplogroup, the same as a common American one, indicates to me the haplogroup entered Africa quite recently from America. It is not a deeply indigenous African haplogroup.

"I looked at the video they said she was of East Asian origin".

I think that was Oscar's mother, wasn't it? I didn't watch the video again but I remember one Maori who was tested was shown to have an Amerindian maternal haplogroup although as far as he knew his mother's family had all come from England.

"The only nonsense here is "almost Denisovan level". Low as it is Amerindian heterozygosity is still about 3 times higher than Denisovans', and is a little more than half of Africans'... so saying Amerindian heterozygosity is "almost Denisovan" is absolute codswallop (to phrase it nicely). "

I keep pointing you to the most recent Lazaridis, which definitively proves me right - Amerindian heterozygosity is closer to Denisovan than to Africans. But in your usual fashion you keep ignoring the data to stay with your belief.

"But "closest" (or "most similar") doesn't always mean "close" (or "similar") - the number 60 is "closest" to 25 out of 60, 70 and 80, but that doesn't make it "close" to 25. Amerindian and Denisovan demographic/genetic structure are not at all similar. You started out using (technically) correct phrases like "most similar" and "closest to" to imply a correlation, and now you are going beyond this and saying they effectively *are* the same with phrases like "almost Denisovan", "is similar to" and "as homozygous as". This is a intentional misrepresentation of the data through deliberate semantic trickery."

How can a "technically correct phrase" be "semantic trickery"?

"It's a logical consequence of high heterozygosity - you can't have high heterozygosity unless you have a high number of derived alleles (think about it!) "

Nonsense. You can get high heterozygosity through recent admixture with an archaic population. So, you don't have a source for your blanket statement?

"As it turns out Loschbour has lower heterozygosity than Amerindians anyway, so your point is moot... unless you now believe we all came from European hunter-gatherers?"

Again, I pointed out to you that the ancient sample from Europe, Loschbour, needs to be compared with an ancient sample from America such as Anzick to compare apples and apples. In any case, the Loschbour examples clearly shows that heterozygosity grows over time and doesn't progressively decline, as out-of-Africa theorists want everyone to believe.

How do you identify "sapient" lineages genetically? The term "sapient" refers to morphology and behavior, not to (neutral) genes. Plus all "anatomically modern human" (another confusing term) skulls in Africa have "archaic" features (absent in truly modern human skulls from 40,000 years down to 10,000 years), so it all depends how and where you "cut" the continuum.

"It was very clear that none of the sources you brought were talking about pre-sapiens populations, and none of them use the word "archaic" anyway, so I find it very hard to believe you were just "confused" and not deliberately trying to present something not supported by the sources."

Again you're ignoring the distinction between what's overtly stated and what constitutes a logical outcomes of a theory. Khoisan clicks and Khoisan/Pygmy music are considered to be "primitive" traits by the proponents of out-of-Africa. These traits have supposedly progressively disappeared in populations outside of Afrcia. Same for skin color.

".. and yet you still haven't explained how your theory that all African diversity can be attested to pre-sapiens admixture does not logically require that Africans be primarily non-sapiens. It seems to be a reasonable conclusion given the presumptions of your theory provided so far."

Out-of-Africa construed Africans as 100% archaic but it called them "modern." It construed non-Africans as modern but called them bottlenecked Africans. In my interpretation, the "modern" (living) and the "archaic" (extinct) are spread across the human continuum from the New World to Africa. You have archaic continuity in the East and you have archaic admixture in the West. Everything is in plain sight. If you prefer to conclude that Africans are "pre-sapiens" in my theory but fully sapient in the out-of-Africa framework, you attribute to me the parlance that I don't use, while repeating what out-of-Africa theorists say without analyzing what the evidence they marshalled in support of their words actually shows.

"If I were fat, bald and ugly too would that make you less of a jerk if you pointed it out? If you have logically consistent reasoning and verifiable facts then present them - nobody's going to change their mind just because you called them names, factual or not (and if you think "bible-basher", "creationist bigot" and "consensus-hugger" are facts, then I suggest you get a better dictionary)"

You obviously reject facts and reasoning and the only rational explanation for why you reject them is because you haven't adopted a scientific worldview. You treat science writing as Scripture and consensus as a collective belief based in revelation. You don't bring independent value into the conversation because you only consume other people's writings. You are ignorant across the whole spectrum of sciences and humanities. I do address these issues of yours head-on. And this is not a personal attack. You aren't even a person, as your real identity is unknown. Calling a person with all the needed credentials "jerk" and "arrogant twerp," however, is.

"I've never denied the science, just your personal interpretation of it, and your "scientific" credentials don't mean you are always right - you still need to use facts and logical reasoning to back up your interpretations."

Yes, I do. Always. But you don't understand them. And this is precisely the behavior seen from creationist bigots.

You JUST fabricated that Amerindian heterozygosity is "almost Denisovan level", and previously that it is "similar to that of Denisovans and Neanderthals" and on another thread that Amerindians are "as homozygous as Denisovans". None of these "facts" are true."

You must have lost your mind. Just open Table S2.2 in the latest Lazaridis and you'll see that Karitiana is far closer to Denisovan than to Yoruba. If you postulate a scenario that requires added heterozygosity from East Asians and Europeans (let's say 7.04 in Han plus 7.38 in French), Karitiana at 4.99 will be close enough to Denisovan 1.82 to make your whole scenario nonsense.

It's an unforgivable mistake not to consider the enormous impact of islamic slave raiding/trading in Africa when contemplating e.g. haplogroup A. From the 8th century and for more than thousand years African slave trade was dominated by Arab-Berbers etc as Islam moved southwards along the Nile and along the desert trails controlled by local Muslims, and Arabs. Another mistake is to neglect/overlook the causes and impact of the much earlier yet little understood Bantu expansion which enslaved, annihilated and resettled the native mongoloid (cold adapted?!) Khoisan/Sandawe speakers. Who were the Bantu speaking newcomers who so recently and quickly multiplied all over sub-Saharan Africa?Personally I think it is quite obvious that the click speaking mongoloids represent an early out of Asia movement long before the Bantu expansion. Also compare Shompen in South Asia.

@German:I keep pointing you to the most recent Lazaridis, which definitively proves me right - Amerindian heterozygosity is closer to Denisovan than to AfricansHow can a "technically correct phrase" be "semantic trickery"?Just open Table S2.2 in the latest Lazaridis and you'll see that Karitiana is far closer to Denisovan than to Yoruba

Nonsense. You can get high heterozygosity through recent admixture with an archaic population.

You do know that "heterozygosity" is a count of sites which have both and ancestral and derived allele right? For a low-heterozygous population to have more derived alleles than a highly heterozygous one, they would need to be fixed (homozygous) for the derived allele in a majority of sites - something which would only apply if the site was under strong selection and the vast majority of sites are non-functional drift.

You might want to also consider that large-scale admixture with a low-heterozygous population can actually *decrease* heterozygosity, since you are getting a host of always-ancestral alleles mixing with only 50%-derived ones - the homozygous parent always gives the ancestral allele while the heteryzygous parent will only gives a derived allele 50% of the time. If the admixture is small and the offspring are brought back to the highly heterozygous population then this will result in new SNPs spreading through the population and thus higher heterozygosity, but if the admixture is large and consistent, marginal alleles can be lost and thus heterozygosity decrease. A case in point are the French, a recent mix of Loschbour and Stuttgart showing a heterozygosity midway between them (a bunch of the 50% derived Stuttgart alleles were replaced by the always ancestral Loschbour ones).

Again, I pointed out to you that the ancient sample from Europe, Loschbour, needs to be compared with an ancient sample from America such as Anzick to compare apples and apples.

Then modern Amerindians need to be compared to modern samples, not 40,000yo Denisovans. Consistency is a bummer hey.

Again you're ignoring the distinction between what's overtly stated and what constitutes a logical outcomes of a theory.

Your "logic" so far is to construe various words that mean "old" as meaning "archaic" in a genetic sense... pure semantics.

Out-of-Africa construed Africans as 100% archaic but it called them "modern."

No it didn't - you did. Out-of-Africa construed Africans to be as "modern" as Europeans, Asians, Americans, Australians, Papuans, Polyesians etc. etc. In contrast Out-of-America posits that Africans have more than 50% archaic admixture.

"It's an unforgivable mistake not to consider the enormous impact of islamic slave raiding/trading in Africa when contemplating e.g. haplogroup A. From the 8th century and for more than thousand years African slave trade was dominated by Arab-Berbers etc as Islam moved southwards along the Nile and along the desert trails controlled by local Muslims, and Arabs."

Most of the Arab/Turkish slave trade was directed at Slavs. The Black Moors in North Africa and Turks in Egypt were mainly engaged in bringing European women to North Africa for their harems.

There were few Sub-Saharans sold into slavery before the Atlantic slave trade.

klevius said...

"Personally I think it is quite obvious that the click speaking mongoloids represent an early out of Asia movement long before the Bantu expansion. Also compare Shompen in South Asia"

The Khoisan are not Mongoloid people. They probably represented the Cro-Magnon expansion into Iberia from North Africa as represented by the Aurignacian and Grimaldi cultures.

I noted earlier that:

There have been numerous "Khoisan skeletons" found in Europe according to Marcellin Boule and Henri Vallois , in Fossil Man (1957). Boule and Vallois reported the find of SSA skeletons at , Grotte des Enfants , Chamblandes in Switzerland , several Ligurian and Lombard tombs of the Metal Ages have also yielded evidences of a Negroid element.

Boule and Vallois (1957), was able to chart the migration of civilization from South Africa to the Aurignacian culture of Europe. These anthropologist reported that the Khoisan shared the same style stone implements and burials 'associated with the Aurignacian or Solutrean type industry...."( Boule and Vallois, 1957, p.318-319). They add, that in relation to Bushman [Khoisan] art " This almost uninterrupted series leads us to regard the African continent as a centre of important migrations which at certain times may have played a great part in the stocking of Southern Europe. Finally, we must not forget that the Grimaldi Negroid skeletons show many points of resemblance with the Bushman [Khoisan] skeletons" (Boule and Vallois,1957).

"You might want to also consider that large-scale admixture with a low-heterozygous population can actually *decrease* heterozygosity..."

In theory this could be true, but in order for this explanation to work, we would have to identify what "low heterozygosity" population contributed to Amerindians. Is it ANE? Has anyone tried measuring the heterozygosity of Mal'ta?

@ German

" In any case, the Loschbour examples clearly shows that heterozygosity grows over time and doesn't progressively decline, as out-of-Africa theorists want everyone to believe."

Well, actually, Out-of-Africa theorists do believe that heterozygosity grows over time, which is why they make such a big fuss about the high heterozygosity of modern Africans. But what they also believe is that heterozygosity declines with distance from Africa due to bottlenecking.In order to explain these results Out-of-Africa theorists would need to come up with some explanation for why Loschbour lost more heterozygosity than Stuttgart. It's noteworthy that Lazaradis' admixture chart does not indicate that Stuttgart is noticeably more African than Loschbour, so it does not appear to be the case that Stuttgart's high heterozygosity is due to more African gene flow.

"Then modern Amerindians need to be compared to modern samples, not 40,000yo Denisovans. Consistency is a bummer hey".

German has almost a monopoly on inconsistency. It is the only thing consistent about him. He's absolutely dripping with it.

"You're not just saying they're closer (irrelevant, but technically correct), you are saying they're actually close (completely false)"

Arguing with German is even less productive that arguing with Maju. Neither will concede they can possibly be wrong in any way, although German is far worse than is Maju. We are all wasting our time arguing with German. He has his belief and is completely against the use of any evidence or logic that proves him wrong. And how does 'homozygosity' relate to 'origin' anyway?

"You can get high heterozygosity through recent admixture with an archaic population".

Yes, you can. And that explains any heterozygosity you see in Amerindians. Admixture, not necessarily 'recent'.

For some twenty years I have proposed the view that modern humans got a small but more efficient brain in the south (jungle?) but that they peaked culturally in the cold north where they got a bigger brain by mixing with pre-existing Homos. Neanderthals contributed with big skulls and erectus with mongoloid traits. We do know that Floresiensis possessed a brain that was much smaller than erectus' brain yet managed to produce similar culture. What is today called Indonesia happened to have the perfect breeding environment for the brain experiment that produced both Floresiensis and Denisovan: Jungles which, due to sea level changes, altered between islands and mainland. When mainland Floresiensis/Denisovans mixed with erectus (Red Deer Cave people might have been such a hybrid) they improved the brain qualities of erectus while getting erectus' mongoloid traits for cold adaptation (assuming erectus got it in their initial expansion to the north as well) and later on brought it south). Somewhere in the Altai region they also encountered northern Neanderthals which further enlarged their heads and produced a very smart modern human (compare the Denisova bracelet) which then started a successful back migration in all directions which strengthened the mongoloid traits in the already mongoloid east while mongoloid traits were diluted when mixing with non-mongoloids in the west and southwest (Neanderthal and archaic sapiens hybrids) and later on by the neolithic expansion. This explains the general racial pattern and also why we have "skinny" mongoloids both in the south and north although the original northern mongoloid were presumably "fatty" for the cold (compare Venus figurines, steatopygia etc).

It's extremely important to distinguish between PC cultural "race" terms and evolutionary traits. I call myself as belonging to the "bastard race", i.e. not a Saami, Scandinavian, Finn or Swede, but with a lot of mongoloid genetic traits in common with them or their predecessors. With a dad born in Gothenburg and a Finnish mother born in Helsinki who delivered me in Stockholm, and with a bilingual upbringing in Finland to a culturally ethnic Atheist Finland-Swede working in both Finland and Sweden, I rather emphasize my ethnicity under the 1948 Universal Human Rights declaration. Which fact effectively keeps my logic out of sexist and racist ranting about my ethnicity/race that would otherwise make it more difficult to produce scientific theories in this field.

Funny, but somehow I never even reflected over other "races" as being "inferior" or "different" as human beings or anything before these self-declared cultural "races" themselves started implying that I also possessed a "race" and that that "white" "race" was a "racist" "race". Had no idea really and in the 1990s while living in Finland and after visiting some "black" and "colored" Swedes in Stockholm our little daughter thought Swedes were black in general.

"Well, actually, Out-of-Africa theorists do believe that heterozygosity grows over time, which is why they make such a big fuss about the high heterozygosity of modern Africans. But what they also believe is that heterozygosity declines with distance from Africa due to bottlenecking.In order to explain these results Out-of-Africa theorists would need to come up with some explanation for why Loschbour lost more heterozygosity than Stuttgart. It's noteworthy that Lazaradis' admixture chart does not indicate that Stuttgart is noticeably more African than Loschbour, so it does not appear to be the case that Stuttgart's high heterozygosity is due to more African gene flow."

This is a very good point. I should've said "out-of-Africa theorists believe that heterozygosity progressively declines outside of Africa," while the Loschbour to Stuttgart example shows that this is not the case. And yes, higher heterozygosity in Stuttgart has nothing to do with their stronger African legacy.

They are closer to Denisovan than to modern Africans. Just take some time to digest this important fact. Of course, Amerindians are more heterozygous than Denisovans - that's the point. It means that Amerindians went through a New World-internal admixture (say, two Denisovan-like ancestral populations), which made them more heterozygous than Denisovans but still less than East Asians, but not an admixture between more heterozygous East Asians and even more heterozygous West Eurasians - an idea you parroted from some misguided academics who don't have a right paradigm to interpret the influx of new data.

"No it didn't - you did. Out-of-Africa construed Africans to be as "modern" as Europeans, Asians, Americans, Australians, Papuans, Polyesians etc. etc. In contrast Out-of-America posits that Africans have more than 50% archaic admixture."

You're confusing again and again the overtly stated tenets of a theory with its logical outcome. Modern Africans were presented by the classic out-of-Africa as the only surviving (African) archaics defined by a host of archaic phenotypical, linguistic and cultural traits which are nearly always LOST in non-Africans (clicks, black skin, really really old, who knows how old but similar-to-gibbon vocalization-old musical styles such as hooted hocket, etc.). For plesiomorphic properties of African teeth (genetically determined traits!) read http://www.ncbi.nlm.nih.gov/pubmed/9467783. Of course, they are going to call them "modern." This is just the politics of race. Needless to say, our self-proclaimed mathematical genius Tobus doesn't need to know anything about "humanities." He's comfortable in his intellectually primate state.

"Then modern Amerindians need to be compared to modern samples, not 40,000yo Denisovans. Consistency is a bummer hey."

Another distorted argument. If there was a 40,000 year old Amerindian sample available, I would've engaged it. But we have to work with modern Amerindians and Anzick for the time being. But Anzick IS available to compare it to Loschbour.

"You do know that "heterozygosity" is a count of sites which have both and ancestral and derived allele right? "

I've been trying not to respond to German's idiocy, but can't resist. Sorry.

"It means that Amerindians went through a New World-internal admixture (say, two Denisovan-like ancestral populations), which made them more heterozygous than Denisovans but still less than East Asians"

What? You're claiming to have 'evidence' yet here you go proposing two different popuklations in America whereas there is a complete absence of any evidence for humans in America at the time of Denisova. And you're proposing TWO different Denisova populations in America! What substance are you smoking? I agree with Annie that your questioning is valid but surely you need to have a little bit of evidence for your own belief. Denisovans themselves were never part of the Amerindian genetic makeup and so the relative heterozygosity of the two populations is completely irrelevant.

"They are closer to Denisovan than to modern Africans. Just take some time to digest this important fact".

The most likely explantion is that Amerindians mixed with a Denisova-derived population while Africans didn't. That is surely simple enough to grasp.

"If there was a 40,000 year old Amerindian sample available, I would've engaged it".

And you don't think that the complete lack of any '40,000 year old Amerindian sample' may indicate something?

Only in a linear sense, in a logarithmic or exponential sense they are closer to modern Africans - they only need to double their heterozygosity to reach an African-level, while Denisovans would need to triple theirs to reach an Amerindian-level.

So should we treat heterozygosity as a linear or exponential property? If you are associating it with demographic history then definitely exponential - a population of 1000 is going to take much longer to get to 2000 than a population of 10,000 will take to get to 11,000, even though the linear difference is the same.

You're confusing again and again the overtly stated tenets of a theory with its logical outcome.

You've yet to produce this "logic" that inevitably leads to the outcome you suggest - all you've done is construe people using the term "ancient" in a cultural sense as though they were meaning "archaic" in a genetic sense, when they quite clearly weren't. There's no logical reason why Africans must be archaic in the Out Of Africa theory. The same cannot be said for your Out Of America though, which as presented requires such a degree of archaic admixture that modern Africans would be less than half homo sapiens.

If there was a 40,000 year old Amerindian sample available, I would've engaged it

It wouldn't make a difference - you'd still be comparing it to a modern population and Loschbour would still be 33,000 years more relevant.

However, my larger point would be to emphasize how so many things can impact heterozygosity, not just the age of the population or distance from Africa. Hence, I remain unconvinced by the model presented by Out-of-Africa supporters, that heterozygosity is high in Africa due to age and that heterozygosity is lost via bottlenecking during migrations away from Africa. The low heterozygosity for Neanderthals would back up my skepticism.

@agiering:my larger point would be to emphasize how so many things can impact heterozygosity, not just the age of the population or distance from Africa

I agree in principle - that there are many factors to consider when finding a cause for heterozygosity, but I think it's important to note that *high* heterozygosity can only come from a long and steady accumulation of genetic mutations, either from drift and/or by acquiring them by admixing with neighbouring populations, and isn't really possible without a large gene pool... so it's much easier for a population to lose heterozygosity than to gain it.

In the case of Africa I suspect heterozygosity is a combination of both sources - we have a number of separate lineages that are in the region of 200,000 years old (so lots of varied drift) and we know that there has been extensive internal migration (and hence mixing) in the last few thousand years if not before. If we contrast this with America where we have lineages <20kya and a population still expanding geographically (so sub-populations don't have to mix in order to expand), it's hardly a surprise that the heterozygosity difference is that way is it.

In regards to Neanderthals I'm not convinced that the samples we have are necessarily representative - the species existed for some 400,000 years and the samples we have are the tail-enders from their last 10,000 years or so. I suspect that in their prime they may have been a lot more populous and showed a lot more diversity than what we see from the highly-inbred samples we have.

Your last post doesn't leave me a whole lot to argue with with (except for maybe your date for the peopling of the Americas).

"I suspect that in their prime they [Neanderthals] may have been a lot more populous and showed a lot more diversity than what we see from the highly-inbred samples we have."

It's possible, but if that scenario were correct, it would demonstrate how much genetic diversity can decline, even without a mass geographic migration. This would only reduce the necessity of positing some continental migration-caused bottleneck to explain the low heterozygosity of non-Africans vs Africans (or Amerindians vs. Eurasians).

"Only in a linear sense, in a logarithmic or exponential sense they are closer to modern Africans - they only need to double their heterozygosity to reach an African-level, while Denisovans would need to triple theirs to reach an Amerindian-level."

You are - as always - debating for the sake of debating. We have only 2 ancient samples and hundreds of modern ones. There surely were ancient populations intermediate between Denisovans and Amerindians. An admixture event between just two Denisovan-like population would make them reach the Amerindian level.

"So should we treat heterozygosity as a linear or exponential property? If you are associating it with demographic history then definitely exponential - a population of 1000 is going to take much longer to get to 2000 than a population of 10,000 will take to get to 11,000, even though the linear difference is the same."

Wrong analogy. The difference between Amerindians and Africans is not similar to the difference between 10,000 to 11,000. But you are again trying to use pseudoscientific reasoning (it used to be "closer" vs. "closest," now it's "linear" vs. "logarithmic") to get out of a factual trap. The pattern I identified is uncontroversial.

@TerryT

"What? You're claiming to have 'evidence' yet here you go proposing two different popuklations in America whereas there is a complete absence of any evidence for humans in America at the time of Denisova. And you're proposing TWO different Denisova populations in America!"

There can be dozens of undetected pinkies hiding in caves in the New World. Remember that's all (plus a tooth) that we have from Denisovans. And we have thousands of years ahead of us to find them. Your counterargument is invalid.

"You've yet to produce this "logic" that inevitably leads to the outcome you suggest - all you've done is construe people using the term "ancient" in a cultural sense as though they were meaning "archaic" in a genetic sense, when they quite clearly weren't. There's no logical reason why Africans must be archaic in the Out Of Africa theory. The same cannot be said for your Out Of America though, which as presented requires such a degree of archaic admixture that modern Africans would be less than half homo sapiens."

I've produced the logic and the evidence, but you've denied them in your usual anti-science fashion to be able to continue with your beliefs. You've started off by claiming that Out-of-America makes Africans look less than half homo sapiens. To this I replied that out-of-Africa treats them as 100% "archaic". Neither I, nor out-of-Africanists explicitly call Africans "pre-sapient" to whatever degree, so it's a matter of analyzing the content of the two theories and making logical conclusions. I provided evidence that out-of-Africanists postulate a number of "archaic" (plesiomorphic) retentions across phenotype, genes and culture that affected only modern Africans (or the most "basal" groups within Africans) and that were lost at the different stages of out-of-Africa evolution. Out-of-Africa hasn't produced any set of DERIVED modern traits which are incipient in modern Africans and fully developed outside of Africa. Under Out-of-America, these "archaic retentions" via modern Africans' common descent with extinct African archiacs are reinterpreted as products of archaic admixture or convergences. By all means, out-of-America treats modern Africans as "more modern" than what's implied by out-of-Africa.

@German:An admixture event between just two Denisovan-like population would make them reach the Amerindian level.

Hardly (it would take nearly three assuming that all their heterozygosity was different and that all of it was retained, in reality it would probably a lot more than three), but consider also that it would only take a small bottleneck event or other genetic disruption to reduce East Asian-like heterozygosity to an Amerindian level.

The difference between Amerindians and Africans is not similar to the difference between 10,000 to 11,000

Correct, I was using an extreme example to make my point clear - that it's more accurate to compare the ratio between the heterozygosity scores, not the raw distance. To rephrase what I said to be proportional to this data: A population of 1820 people is going to take longer to reach 4990 (a 2.75x increase) than a population of 4990 people will take to reach 9780 (a 1.95x increase), despite the what raw figures (3170 and 4730) might lead you to think.

I've produced the logic and the evidence

You produced the logic, but the evidence was just misinterpreting words that mean "old" to mean "archaic" in a genetic sense - none of the sources you provided actually supported what you are saying, and it one case flat-out rejected it.

By all means, out-of-America treats modern Africans as "more modern" than what's implied by out-of-Africa.

That's certainly not a universal or mainstream interpretation, but you are welcome to continue believing it if it makes you happy.

@German:East Asian heterozygosity multiplied by West Eurasian heterozygosity and then reduced to nearly Mid-Pleistocene level.

There's that lie again! Amerindian heterozygozity is nowhere near mid-Pleistocene level, and you know it. In case you forgot the mlrho theta for Amerindians is 5.65 on Prufer, about 300% higher than Denisovan-level (1.88) and only 25% less than Han/Dai level (7.31)... I've had to correct you on this issue multiple times now, please stop repeating what you know is incorrect.

This relatively small decline we see in Amerindian heterozygosity is exactly what we'd expect from a genetic disruption like a bottleneck event. Remember also that we're talking about MA-1's heterozygozity not modern European's - it was likely lower than modern Amerindian heterozygosity to begin with.

It's very very believable, even most natural.

That admixture between two extremely low-heterozygous populations would create a heterozygosity level some 3 times higher than either of them?!?... Sounds extremely far-fetched to me.

"There's that lie again! Amerindian heterozygozity is nowhere near mid-Pleistocene level, and you know it. In case you forgot the mlrho theta for Amerindians is 5.65 on Prufer, about 300% higher than Denisovan-level (1.88) and only 25% less than Han/Dai level (7.31)... I've had to correct you on this issue multiple times now, please stop repeating what you know is incorrect."

What lie? You need to recalibrate your meds, Tobus. The numbers logic you quote - which, in general, fully support out-of-America - have no bearing on my statement that Amerindian population structure is of mid-Pleistocene extraction. Mid-Pleistocene populations in Eurasia may have ranged from 1.88 to 5.66 and Amerindians would fall into that bracket. Unlike East Asians who would be close to it but no cigar. My statement is just a recap of Zhivotovsky and Cavalli-Sforza's interpretation of Amerindian demographics, which you likely have too short a memory to remember. the Prufer and Lazaridis data fully support it.

"That admixture between two extremely low-heterozygous populations would create a heterozygosity level some 3 times higher than either of them?!?... Sounds extremely far-fetched to me."

I know evolution is a thing that's hard to believe in. The ex nihilo creation of a highly heterozygous African population with subsequent fall from grace through bottlenecks is much easier.

"Did you present some facts?"

Of course I did. Did out-of-Africanists do the same thing? Or they just thought they could ride off the coattails of cultural mythology?

@German:Mid-Pleistocene populations in Eurasia may have ranged from 1.88 to 5.66 and Amerindians would fall into that bracket

Then what makes it "Nonsense" that Amerindian heterozygosity could be reduced to this apparently very normal and widespread level? Seems like it would be quite expected if that was the level of their ancestral populations at the time no?

I know evolution is a thing that's hard to believe in.

I don't have any problem believing in it - all the facts point there. Funny that you repeatedly claim that I'm making "creationist" arguments when it's you that has trouble understanding one of the basic tenets of modern scientific theory.

...fall from grace...

?? You seem to think some populations are "better" ("holier"?) than others based on their ancestry - that a recent divergence or lower diversity somehow equates to a "fall from grace" or some other form of inferiority. I think you need to do some "anthropologising" on yourself in this regard - it's probably part of the issue that's holding you back. Amerindian culture and lifestyle is just as valid and interesting whether it's 10,000 years old or 100,000, you can still worship them (or however you want to describe your obsession) even if they're not the ultimate ancestors of all modern humans.

"Then what makes it "Nonsense" that Amerindian heterozygosity could be reduced to this apparently very normal and widespread level? Seems like it would be quite expected if that was the level of their ancestral populations at the time no?"

10,000 years ago (after presumably 40,000 years of diversity accumulation) a highly derived population suddenly drops to the level of an ancestral population. After having admixed with another highly derived population. Pseudoscience.

"one of the basic tenets of modern scientific theory."

Science evolves - that's the basic tenet. Only religion is based on an initial revelation which makes newly discovered facts irrelevant unless they explicitly reinforce the revelation.

"You seem to think some populations are "better" ("holier"?) than others based on their ancestry."

No, but the use of biblical metaphors best describes the inner workings of your pseudoscientific mind. Highly heterozygous.

"This relatively small decline we see in Amerindian heterozygosity is exactly what we'd expect from a genetic disruption like a bottleneck event".

Possibly as much to do with the lack of any reasonable level of admixture with other populations after becoming isolated as well. We are becoming aware from genetic studies that there has been considerable movement around Eurasia and Africa. And even into New Guinea.

"Did you present some facts?"

I can't remember any either.

" My statement is just a recap of Zhivotovsky and Cavalli-Sforza's interpretation of Amerindian demographics, which you likely have too short a memory to remember. the Prufer and Lazaridis data fully support it".

Really? I don't remember any of them claiming humans came out of America. I grant it is probably possible to intentionally misrepresent their work to make it look as though they meant to say that humans had come from America.

"I know evolution is a thing that's hard to believe in".

Certainly to you it seems to be so, but others of us understand it readily enough. You seem unable to accept evolution involves changes in genes, not sudden miraculous creations. Genetic changes can come about through mutations in an existing genetic structure but the vast majority of new mutations are neutral, and most of the remainder are deleterious. That leaves very few advantageous one, and these few tried and tested genes are usually spread by population mixing. We now know that modern Europeans, for example, differ from earlier Europeans more through immigration of new populations rather than through genetic mutation and selection within the 'original' European population.

"The ex nihilo creation of a highly heterozygous African population"

Hang on a minute. I just replied to one of your comments elsewhere where you appear to believe in the ex nihilo creation of not one but two American populations: one with EDAR370A and one without. I have come to accept that consistency is not your strong point of course. You just interpret data the way you want to, with no consideration of the wider picture.

@German:10,000 years ago (after presumably 40,000 years of diversity accumulation) a highly derived population suddenly drops to the level of an ancestral population

Except that we have evidence of a 7,000 year old population with an even lower level... and we have a number of other modern populations with levels only a few percent higher. So this level was evidently not so "ancestral" at all, and certainly within the bounds of expectation for a population which recently migrated through some of the most inhospitable environment humans can survive in.

"Except that we have evidence of a 7,000 year old population with an even lower level... and we have a number of other modern populations with levels only a few percent higher."

Well, the 7,000 year old population in Europe, with a clear sign of Amerindian admixture, supports the notion that ancestral levels of homozygosity were much more frequent in the past in association with New World and New World-derived populations in the Old World.

"with levels only a few percent higher."

Sure, levels of homozygosity in the Old World follow the logic of genetic affinity with Amerindians.

" within the bounds of expectation for a population which recently migrated through some of the most inhospitable environment humans can survive in. "

Rather stayed put in most inhospitable environment humans and their hominin antecedents such as Denisovans and Neandertals could survive in for tens of thousands of years.

"Sorry, what signs of Amerindian admixture? All evidence points to Amerindians having Eurasian admixture, not the other way round."

In another thread, Tobus is reluctantly admitting that all Eurasians are Amerindian shifted. Apparently, there are two Tobuses around here: one who reluctantly admits that the Earth rotates around the Sun and the other who thinks that all evidence points to the Sun rotating around the Earth.

"In another thread, Tobus is reluctantly admitting that all Eurasians are Amerindian shifted".

Everyone accepts 'all Eurasians are Amerindian shifted'. The reason is that Amerindians share ancestry with both East and West Eurasians. They are a mix of the two. It requires extremely convoluted 'reasoning' to make Amerindians ancestral to both East and West Eurasians. A convoluted argument that only you are prepared to indulge in. In other words you are the one here who is arguing the sun goes round the earth.

@German:In another thread, Tobus is reluctantly admitting that all Eurasians are Amerindian shifted.

As terry pointed out, an "Amerindian shift" on a particular is not necessarily proof of "Amerindian admixture".

It's clear that Amerindians have West Eurasian admixture, not that Europeans have Amerindian admixture. The direction of the "shift" on any particular charts depends on which population is the reference - eg Olalde 5a has Europeans shifted towards Amerindians on the X (Karitiana) axis, but Amerindians shifted towards Europeans on the Y (Sardinian) axis.

Precisely the opposite. Amerindians don't have any of the MA-1 components but the Amerindian one, which means they postdate the appearance of the Amerindian component in East Asia. Neither do they have the mtDNA or Y-DNA lineages found in MA-1. West Eurasians, ancient and modern, have "Amerindian" affinity. This is what the other Tobus admitted - "all of Eurasians have Amerindian affinity." And Patterson et al. refer to the phenomenon as "Amerindian admixture."

"The direction of the "shift" on any particular charts depends on which population is the reference - eg Olalde 5a has Europeans shifted towards Amerindians on the X (Karitiana) axis, but Amerindians shifted towards Europeans on the Y (Sardinian) axis."

Amerindians are more divergent from West Eurasians on their axis than West Eurasians from Amerindians on theirs.

"All it means is that modern Amerindians are the "best fit" for about 30% of MA-1s DNA."

And how does it contradict what I said? the Amerindian 30% of MA-1 DNA is ancestral, all others post-date the migration from the Americas, hence they are not found in the Americas. Are you still planning to get a degree?

"Amerindians get the same score (~0.16) on the Sardinian axis that Europeans get on the Karitiana one - as I explained to you earlier, this a function of how the f3 maths works."

Yes. That's exactly how I explained to you the mutual relationship between MA-1 and Amerindians. But Amerindians get a higher score on their axis than Europeans on theirs. It means they are effectively more divergent than West Eurasians. I don't think getting a degree is a wise use of your time.

Getting a degree was certainly not a wise use of your time if your objective was to understand genetics or evolutionary biology. But perhaps your objective was to gain a living in the marketing sector.

It doesn't contradict it, it just points out that your conclusion isn't a logical inference from the data - to wit "Amerindians don't have any of the MA-1 components but the Amerindian one, which means they postdate the appearance of the Amerindian component in East Asia"... Amerindians not having an MA-1 components means no such thing - the components are modern ones retrofitted, so the Amerindian one could certainly have arisen after the others. You made a arbitrary conclusion and are stating as a proven fact.

But Amerindians get a higher score on their axis than Europeans on theirs. It means they are effectively more divergent than West Eurasians

It means they have more common shared drift than Europeans/East Asian despite having the same branch length temporally, and being less genetically diverse. This is consistent with them receiving DNA from two separate post-Yoruba branches, in fact it's hard to reconcile any other way.

"It means they have more common shared drift than Europeans/East Asian despite having the same branch length temporally, and being less genetically diverse. This is consistent with them receiving DNA from two separate post-Yoruba branches, in fact it's hard to reconcile any other way."

The "other way" is the one to reconcile it. Your idea is total nonsense: two highly divergent and heterozygous branches coming together in one population would make it very genetically diverse. But instead we see Amerindians forming a single highly homozygous cluster of high divergence from the European and East Asian clusters.

""Amerindians don't have any of the MA-1 components but the Amerindian one, which means they postdate the appearance of the Amerindian component in East Asia"... Amerindians not having an MA-1 components means no such thing - the components are modern ones retrofitted, so the Amerindian one could certainly have arisen after the others. You made a arbitrary conclusion and are stating as a proven fact."

Back to the UFO idea? You are trying to correct my "arbitrariness" with science fiction.

" two highly divergent and heterozygous branches coming together in one population would make it very genetically diverse".

Not if it subsequently underwent a population bottleneck. But, of course, you don't understand genetics or evolutionary biology and so we have come to expect nonsense from you.

"we see Amerindians forming a single highly homozygous cluster of high divergence from the European and East Asian clusters".

I presume that with this comment you are joking. I was under the impression you have seriously been proposing that both Europeans and East Asians descend from Amerindians but if Amerindians are a 'single highly homozygous cluster' they cannot possibly be ancestral to any populations highly divergent from them.

"You are trying to correct my 'arbitrariness'.

Now it all makes sense. Your objective is just to arbitrarily offer conflicting interpretations of various data just as some sort of private joke.

@German:Your idea is total nonsense: two highly divergent and heterozygous branches coming together in one population would make it very genetically diverse

Loshbour proves these populations were *not* particularly heterozygous at all - you are projecting (and overstating!) modern traits onto ancient populations.

On top of this Schiffels proves (yet again!) that Amerindians underwent a bottleneck that the other lineages didn't, thus reducing their heterozygosity relative to the others - you are ignoring solid and repeatedly confirmed data.

You are trying to correct my "arbitrariness" with science fiction.

Did you actually read the paper on how ADMIXTURE works? Please do, I'm sure you will find it enlightening and it should clear up the obvious misconceptions you have about how to interpret it's results.

"Loshbour proves these populations were *not* particularly heterozygous at all - you are projecting (and overstating!) modern traits onto ancient populations."

We're comparing apples to apples. Modern Amerindians to modern East Asians + Europeans. Loschbour proves that ancient Europeans were more like Amerindians, rather than the other way around. You're trying to hijack a piece of evidence that blatantly contradicts out-of-Africa and supports out-of-America. Good try but no cigar!

"On top of this Schiffels proves (yet again!) that Amerindians underwent a bottleneck that the other lineages didn't, thus reducing their heterozygosity relative to the others - you are ignoring solid and repeatedly confirmed data."

There's no such proof there. Amerindians share the same "bottleneck situation" with Denisovans and Neandertals and the rest of modern humans moved away from ancestral homozygosity best preserved in modern Amerindians.

@German:Loschbour proves that ancient Europeans were more like Amerindians

So, by your spurious logic, Amerindians must be derived from Loschbour!

There's no such proof there. Amerindians share the same "bottleneck situation" with Denisovans and Neandertals and the rest of modern human

From the abstract: "..and give information about human population history as recently as 2,000 years ago, including the bottleneck in the peopling of the Americas, and separations within Africa, East Asia and Europe."

... and P4: "For the Mexican ancestors we see an extended period of low population size following the out of Africa bottleneck, with the lowest value around 15kya, which is particularly pronounced when filtering out genomic regions of recent European ancestry due to admixture (dashed line in Figure 3, see Online Methods). This extended bottleneck is consistent with estimates of the time that the Native American ancestors crossed the Bering Strait and moved into America"

@German:No, Loschbour ultimately derives from an Amerindian population

But he has *lower* heterozygosity than Amerindians!!! He's exactly the same as Denisovans!!!!! He *MUST* be the origin of all mankind!!!!!

They are wrong

I see. Umm... you want to maybe get your own research on the topic published in a highly respected peer-reviewed journal before you make such a grandiose statement? ... I assume you have a whole bunch of robust empirical evidence to back it up?

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